update all Linux images: musllinux_1_2, manylinux_2_28 + fix musllinux segfaults

.github/workflows/build_wheels.yml

@@ -160,7 +160,7 @@ jobs:
         run: |
           echo "CI_ONLY" $CI_ONLY
           if [ "$CI_ONLY" == "true" ]; then
-            MATRIX="[{'only':'cp313-manylinux_x86_64','os':'ubuntu-20.04'},{'only':'cp313-manylinux_aarch64','os':'ubuntu-22.04-arm'},{'only':'cp313-musllinux_aarch64','os':'ubuntu-22.04-arm'},{'only':'cp313-win_amd64','os':'windows-2019'},{'only':'cp313-win_arm64','os':'windows-2019'},{'only':'cp313-macosx_x86_64','os':'macos-13'}, {'only':'cp313-macosx_arm64','os':'macos-14'}]"
+            MATRIX="[{'only':'cp313-manylinux_x86_64','os':'ubuntu-20.04'},{'only':'cp313-manylinux_aarch64','os':'ubuntu-22.04-arm'},{'only':'cp313-musllinux_x86_64','os':'ubuntu-22.04'},{'only':'cp313-musllinux_aarch64','os':'ubuntu-22.04-arm'},{'only':'cp313-win_amd64','os':'windows-2019'},{'only':'cp313-win_arm64','os':'windows-2019'},{'only':'cp313-macosx_x86_64','os':'macos-13'}, {'only':'cp313-macosx_arm64','os':'macos-14'}]"
           else
             MATRIX=$(
               {

pyproject.toml

@@ -88,7 +88,6 @@ skip = ["*-win32", "*_i686",  # skip 32-bit builds
         "pp37-*",             # skip certain PyPy configurations
 	"pp*_aarch64 ",       # no numpy wheels for aarch64 on PyPy
 	"pp311-*",            # no numpy wheels for PyPy 3.11
-        "cp313-musllinux_x86_64", # no lxml wheels for  musllinux_1_1 on cp313
         "cp36-musllinux_*", "cp37-musllinux_*", "cp38-musllinux_*"] # older musllinux missing numpy wheels
 test-skip = ["*-win_arm64", "cp38-macosx_arm64"]
 test-extras = ["test"]
@@ -109,6 +108,11 @@ build-frontend = { name = "pip", args = ["--only-binary=:none:"] }
 archs = ["auto", "aarch64"]
 # default linux wheels use CentOS-based runners, local cibuildwheel docker
 before-all = ["yum install -y gsl-devel"]
+# force use of newer `manylinux_2_28`: in cibuildwheel >= 3.0 it will be the default
+manylinux-x86_64-image = "manylinux_2_28"
+manylinux-pypy_x86_64-image = "manylinux_2_28"
+manylinux-aarch64-image = "manylinux_2_28"
+manylinux-pypy_aarch64-image = "manylinux_2_28"
 
 [[tool.cibuildwheel.overrides]]
 # run the benchmarking only on cp313
@@ -121,14 +125,10 @@ test-command = "pytest --pval-benchmarking -v {package}/tests ${PYTEST_OPTIONS}"
 # musl uses apk/apt
 select = "*musllinux*"
 before-all = ["apk add gsl-dev"]
-# restore musllinux_1_1 image for the time being (musllinux_1_2 segfaults)P
-musllinux-x86_64-image="musllinux_1_1"
-
-[[tool.cibuildwheel.overrides]]
-# use the recent `muslinux_1_2` on cp313
-# lxml for musllinux_1_1 does not exist for Python 3.13
-select = "cp313-musllinux_x86_64"
-musllinux-x86_64-image="musllinux_1_2"
+# FIXME: if we want to run the full tests, need to enable the below to force
+# musllinux_1_1 image for the time being on x86_64 (musllinux_1_2 segfaults on
+# any test involving emhaplofreq)
+# musllinux-x86_64-image="musllinux_1_1"
 
 [tool.cibuildwheel.macos]
 # use oras to get archived 2.7.1 bottles of `gsl` that has 10.15 (on x86) / 11.0 (on arm64) builds

src/PyPop/Haplo.py

@@ -372,7 +372,7 @@ def _runEmhaplofreq(
         permutationFlag=None,
         permutationPrintFlag=0,
         numInitCond=50,
-        numPermutations=1001,
+        numPermutations=1,
         numPermuInitCond=5,
         haploSuppressFlag=None,
         showHaplo=None,
@@ -384,7 +384,8 @@ def _runEmhaplofreq(
         Format of 'locusKeys' is a string as per estHaplotypes():
 
         - permutationFlag: sets whether permutation test will be
-          performed.  No default.
+          performed.  No default. This should only be set if
+          numPermutation is non-zero.
 
         - permutationPrintFlag: sets whether the result from
           permutation output run will be included in the output XML.
@@ -394,7 +395,7 @@ def _runEmhaplofreq(
           performing the permutation test. Default: 50.
 
         - numPermutations: sets number of permutations that will be
-          performed if 'permutationFlag' *is* set.  Default: 1001.
+          performed if 'permutationFlag' *is* set.  Default: 1.
 
         - numPermuInitConds: sets number of initial conditions tried
           per-permutation.  Default: 5.
@@ -664,6 +665,7 @@ def allPairwise(
         else:
             permuMode = "no-permu"
             permutationFlag = 0
+            numPermutations = 1  # FIXME: this translates to being max_permu in C program, needs to be at least one
 
         if mode is None:
             mode = "all-pairwise-ld-" + permuMode

src/emhaplofreq/emhaplofreq.c

@@ -59,8 +59,8 @@ FILE *parse_args(int, char **, int *);
 /* argc, argv */
 /* returns open filehandle of input file */
 
-int read_infile(FILE *, char[MAX_ROWS][NAME_LEN],
-                char[MAX_ROWS][MAX_COLS][NAME_LEN], int *, char[1], char[1]);
+int read_infile(FILE *, char (*)[NAME_LEN], char (*)[MAX_COLS][NAME_LEN], int *,
+                char[1], char[1]);
 /* open filehandle for data, ref array, data array, number of records */
 /* returns number of loci */
 
@@ -70,8 +70,8 @@ int main_proc(
 #else
     FILE *fp_out,
 #endif
-    char[MAX_ROWS][MAX_COLS][NAME_LEN], int, int, int, int, int, int, int, int,
-    int, char[1], char[1]);
+    char (*)[MAX_COLS][NAME_LEN], int, int, int, int, int, int, int, int, int,
+    char GENOTYPE_SEPARATOR[], char GENOTYPE_TERMINATOR[]);
 /* data array, number of loci, number of records */
 /* main procedure that handles memory allocation and creation of arrays,
  * spawns the rest of the data preparation and processing functions,
@@ -115,35 +115,37 @@ void linkage_diseq(FILE *, double *, int (*)[MAX_LOCI], double (*)[MAX_ALLELES],
  * compute LD coefficients
  */
 
-void sort2bychar(char (*)[], double *, int);
+void sort2bychar(char (*)[LINE_LEN / 2], double *, int);
 /* haplo array, mle array, no. of haplotypes */
 /*
  * insertion sort in ascending order for 1st array also applied to 2nd array
  */
 
-void sort2byfloat(char (*)[], double *, int);
+void sort2byfloat(char (*)[LINE_LEN / 2], double *, int);
 /* haplo array, mle array, no. of haplotypes */
 /*
  * insertion sort in ascending order for 2nd array also applied to 1st array
  */
 
 void emcalc(int *, int *, double *, double *, int, int, int, int, int *,
-            int (*)[], int *, int *, double *, double *, int, int (*)[]);
+            int (*)[2], int *, int *, double *, double *, int,
+            int (*)[MAX_ROWS]);
 /* numgeno, obspheno, freq_zero, mle, n_haplo, n_unique_geno,
    n_unique_pheno, n_recs, xhaplo, xgeno, error_flag, iter_count, loglike,
    permu, gp */
 /*
  * perform EM iterations with results in the mle array
  */
 
-void haplo_freqs_no_ld(double *, double (*)[], int (*)[], int *, int, int);
+void haplo_freqs_no_ld(double *, double (*)[MAX_ALLELES], int (*)[MAX_LOCI],
+                       int *, int, int);
 /* freqs, allele_freq, haplocus, n_unique_allele, n_loci, n_haplo */
 /*
  * compute haplotype frequencies under no LD as products of allele frequencies
  */
 
-double loglikelihood(int *, double *, int *, int, int, int, int *, int (*)[],
-                     int, int (*)[]);
+double loglikelihood(int *, double *, int *, int, int, int, int *, int (*)[2],
+                     int, int (*)[MAX_ROWS]);
 /* numgeno, hap_freq, n_haplo, n_unique_geno, n_unique_pheno, xhaplo, xgeno,
  * permu, gp */
 /*
@@ -414,8 +416,13 @@ int main_proc(
   int permu_count; // RS 20031125
   double lr_mean, lr_sd, lr_z;
 
-  CALLOC_ARRAY_DIM1(double, like_ratio, max_permu);
-  CALLOC_ARRAY_DIM1(int, error_flag_permu, max_permu); // RS 20031125
+  /* FIXME: size of array needs be at least one because there is always at least
+   * one like_ratio */
+  /* this should ideally use the logic further down which sets max_permutations
+     to 1 if permutation test not run */
+  int permu_alloc_size = (max_permu > 0) ? max_permu : 1;
+  CALLOC_ARRAY_DIM1(double, like_ratio, permu_alloc_size);
+  CALLOC_ARRAY_DIM1(int, error_flag_permu, permu_alloc_size); // RS 20031125
 
   double pvalue = 0.0;
 
@@ -501,7 +508,8 @@ int main_proc(
         n_hetero++;
         if (strcmp(data_ar[0][col_0], data_ar[0][col_1]) > 0) {
           strcpy(buff, data_ar[0][col_0]);
-          strcpy(data_ar[0][col_0], data_ar[0][col_1]);
+          memmove(data_ar[0][col_0], data_ar[0][col_1],
+                  strlen(data_ar[0][col_1]) + 1);
           strcpy(data_ar[0][col_1], buff);
         }
       }
@@ -563,7 +571,8 @@ int main_proc(
 
         if ((strcmp(data_ar[obs][col_0], data_ar[obs][col_1])) > 0) {
           strcpy(buff, data_ar[obs][col_0]);
-          strcpy(data_ar[obs][col_0], data_ar[obs][col_1]);
+          memmove(data_ar[obs][col_0], data_ar[obs][col_1],
+                  strlen(data_ar[obs][col_1]) + 1);
           strcpy(data_ar[obs][col_1], buff);
         }
 
@@ -1380,7 +1389,7 @@ void linkage_diseq(FILE *fp_out, double(*mle), int (*hl)[MAX_LOCI],
 /* af: allele_frequencies array */
 {
   int i, j, k, l, m, coeff_count = 0;
-  double dmax, norm_dij = 0.0;
+  double dmax = 0.0, norm_dij = 0.0;
 
   static double dij[MAX_LOCI * (MAX_LOCI - 1) / 2][MAX_ALLELES][MAX_ALLELES];
 

tests/base.py

@@ -34,6 +34,7 @@
 """This is a class of common functions for running PyPop tests"""
 
 import os.path
+import platform
 import shutil
 import subprocess
 import sys
@@ -49,6 +50,84 @@
     reason="certain tests currently fail on windows due to minor numerical issues",
 )
 
+
+def is_check_musllinux_enabled():
+    return False
+
+
+# FIXME: this is a somewhat hacky check to see if on musllinux
+def is_musllinux():
+    """Check if running on a musl-based Linux system."""
+
+    if sys.platform != "linux":
+        return False
+
+    # Check if `ldd` output contains 'musl'
+    try:
+        output = subprocess.check_output(
+            ["ldd", "--version"], stderr=subprocess.STDOUT, text=True
+        )
+        if "musl" in output:
+            return True
+    except Exception:
+        pass  # `ldd` might not exist
+
+    # Fallback: Check if running on Alpine (common musl distribution)
+    try:
+        with open("/etc/os-release") as f:
+            if "ID=alpine" in f.read():
+                return True
+    except FileNotFoundError:
+        pass
+
+    return False
+
+
+def debug_musllinux_check():
+    if not is_check_musllinux_enabled():
+        return
+
+    """Print debug info about musllinux detection."""
+    print("=== musllinux detection debug ===")
+    print(f"sys.platform: {sys.platform}")
+    print(f"platform.libc_ver(): {platform.libc_ver()}")
+    print(f"platform.machine(): {platform.machine()}")
+    print("===============================")
+
+    # Run `ldd --version` to check if it's musl
+    try:
+        output = subprocess.check_output(
+            ["ldd", "--version"], stderr=subprocess.STDOUT, text=True
+        )
+        print("ldd --version output:")
+        print(output.strip())
+    except Exception as e:
+        print(f"ldd check failed: {e}")
+
+    # Check `/etc/os-release`
+    try:
+        with open("/etc/os-release") as f:
+            print("/etc/os-release contents:")
+            print(f.read().strip())
+    except FileNotFoundError:
+        print("/etc/os-release not found")
+
+    print("===============================")
+
+    if is_musllinux() and platform.machine() == "x86_64":
+        print("Skipping test due to musllinux_1_2 on x86_64")
+
+
+# call the debug function before applying the skip
+debug_musllinux_check()
+
+# global skip condition for musllinux on x86_64
+# FIXME: currently disabled, to re-enable, change "False" to "True" in condition
+skip_musllinux_x86_64 = pytest.mark.skipif(
+    is_check_musllinux_enabled() and is_musllinux() and platform.machine() == "x86_64",
+    reason="certain tests segfault or fail on musllinux/x86_64, so skipping for now",
+)
+
 CUR_DIR = Path(__file__).parent.resolve()
 PARENT_DIR = Path(CUR_DIR) / ".."
 sys.path.append(PARENT_DIR)

tests/test_AlleleColon.py

@@ -3,6 +3,7 @@
 from base import (
     in_temp_dir,  # noqa: F401
     run_pypop_process,
+    skip_musllinux_x86_64,
 )
 
 
@@ -21,6 +22,7 @@ def test_AlleleColon_HardyWeinberg():
         )
 
 
+@skip_musllinux_x86_64
 def test_AlleleColon_Emhaplofreq():
     exit_code = run_pypop_process(
         "./tests/data/Test_Allele_Colon_Emhaplofreq.ini",

tests/test_ManyOptions.py

@@ -4,10 +4,12 @@
 from base import (
     in_temp_dir,  # noqa: F401
     run_pypop_process,
+    skip_musllinux_x86_64,
 )
 
 
 @pytest.mark.slow
+@skip_musllinux_x86_64
 def test_ManyOptions():
     generated_filenames = [
         "BIGDAWG_SynthControl_Data_with_metadata-" + suffix

tests/test_USAFEL.py

@@ -9,6 +9,7 @@
     filecmp_list_of_files,
     in_temp_dir,  # noqa: F401
     run_pypop_process,
+    skip_musllinux_x86_64,
     xfail_windows,
 )
 
@@ -83,6 +84,7 @@ def test_USAFEL_slatkin_guothompson():
     assert filecmp_ignore_newlines(out_filename, gold_out_filename)
 
 
+@skip_musllinux_x86_64
 def test_USAFEL_slatkin_guothompson_emhaplofreq():
     exit_code = run_pypop_process(
         "./tests/data/minimal.ini", "./tests/data/USAFEL-UchiTelle-small.pop"
@@ -98,6 +100,7 @@ def test_USAFEL_slatkin_guothompson_emhaplofreq():
 # FIXME: error in one-line of 2-locus-haplo.tsv on Windows
 # ld.d is 0.01563 rather than 0.01562
 @xfail_windows
+@skip_musllinux_x86_64
 def test_USAFEL_slatkin_guothompson_emhaplofreq_with_permu_tsv():
     exit_code = run_pypop_process(
         "./tests/data/minimal-with-permu.ini",

tests/test_UserGuideExamples.py

@@ -1,9 +1,11 @@
 from base import (
     in_temp_dir,  # noqa: F401
     run_pypop_process,
+    skip_musllinux_x86_64,
 )
 
 
+@skip_musllinux_x86_64
 def test_DataMinimalNoHeaderNoIDs():
     exit_code = run_pypop_process(
         "./tests/data/doc-examples/config-minimal-example.ini",
@@ -13,6 +15,7 @@ def test_DataMinimalNoHeaderNoIDs():
     assert exit_code == 0
 
 
+@skip_musllinux_x86_64
 def test_DataMinimalNoHeader():
     exit_code = run_pypop_process(
         "./tests/data/doc-examples/config-minimal-example.ini",